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- PDB-1hne: Structure of human neutrophil elastase in complex with a peptide ... -

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Basic information

Entry
Database: PDB / ID: 1hne
TitleStructure of human neutrophil elastase in complex with a peptide chloromethyl ketone inhibitor at 1.84-angstroms resolution
Components
  • HUMAN LEUCOCYTE ELASTASE
  • METHOXYSUCCINYL-ALA-ALA-PRO-ALA CHLOROMETHYL KETONE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / pyroptotic inflammatory response / neutrophil-mediated killing of gram-negative bacterium / Activation of Matrix Metalloproteinases / cytokine binding / positive regulation of MAP kinase activity / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / positive regulation of smooth muscle cell proliferation / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / protein catabolic process / positive regulation of immune response / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / azurophil granule lumen / transcription corepressor activity / peptidase activity / heparin binding / : / protease binding / response to lipopolysaccharide / endopeptidase activity / defense response to bacterium / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
methoxysuccinyl-alanyl-alanyl-prolyl-alanine chloromethyl ketone / Neutrophil elastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.84 Å
AuthorsNavia, M.A. / Mckeever, B.M. / Springer, J.P. / Lin, T.-Y. / Williams, H.R. / Fluder, E.M. / Dorn, C.P. / Hoogsteen, K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structure of human neutrophil elastase in complex with a peptide chloromethyl ketone inhibitor at 1.84-A resolution.
Authors: Navia, M.A. / McKeever, B.M. / Springer, J.P. / Lin, T.Y. / Williams, H.R. / Fluder, E.M. / Dorn, C.P. / Hoogsteen, K.
History
DepositionApr 10, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: HUMAN LEUCOCYTE ELASTASE
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA CHLOROMETHYL KETONE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)23,7972
Polymers23,7972
Non-polymers00
Water4,053225
1
E: HUMAN LEUCOCYTE ELASTASE
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA CHLOROMETHYL KETONE INHIBITOR

E: HUMAN LEUCOCYTE ELASTASE
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA CHLOROMETHYL KETONE INHIBITOR

E: HUMAN LEUCOCYTE ELASTASE
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA CHLOROMETHYL KETONE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)71,3916
Polymers71,3916
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Unit cell
Length a, b, c (Å)74.530, 74.530, 70.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein HUMAN LEUCOCYTE ELASTASE


Mass: 23319.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase
#2: Protein/peptide METHOXYSUCCINYL-ALA-ALA-PRO-ALA CHLOROMETHYL KETONE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 476.952 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: methoxysuccinyl-alanyl-alanyl-prolyl-alanine chloromethyl ketone
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND FORM OF THE INHIBITOR (CHAIN I) IS METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE. ...THE UNBOUND FORM OF THE INHIBITOR (CHAIN I) IS METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL ALV AND 2) A COVALENT BOND TO NE2 OF HIS 57
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 262.17178-17181 1987
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.8 Mammonium sulfate1drop
310 mMsodium acetate1drop
41.5 Mammonium sulfate1reservoir
510 mMsodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.84 Å
Reflection
*PLUS
Highest resolution: 1.84 Å / Rmerge(I) obs: 0.165

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.164 / Highest resolution: 1.84 Å
Refinement stepCycle: LAST / Highest resolution: 1.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 225 1892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d0.038
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 16828 / Highest resolution: 1.84 Å / Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.03

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